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DAMASK_EICMD
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This commit is contained in:
Martin Diehl 2016-03-03 14:53:55 +01:00
parent 76a0a93c42
commit a51f2a29f6
4 changed files with 42 additions and 93 deletions
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5
processing/misc/ang_toTable.py
View File

@ -1,8 +1,7 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys,string,vtk import os
import numpy as np
from optparse import OptionParser from optparse import OptionParser
import damask import damask
@ -48,7 +47,7 @@ for name in filenames:
table.labels_append(['1_Euler','2_Euler','3_Euler', table.labels_append(['1_Euler','2_Euler','3_Euler',
'1_pos','2_pos', '1_pos','2_pos',
'IQ','CI','PhaseID','Intensity','Fit', 'IQ','CI','PhaseID','Intensity','Fit',
], # labels according to OIM Analysis 7.2 Manual, p 403 (of 517) ], # OIM Analysis 7.2 Manual, p 403 (of 517)
reset = True) reset = True)
# ------------------------------------------ assemble header --------------------------------------- # ------------------------------------------ assemble header ---------------------------------------

64
processing/misc/calculateAnisotropy.py
View File

@ -1,9 +1,9 @@
#!/usr/bin/python #!/usr/bin/python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import threading,time,os,subprocess,shlex,string import threading,os,string
import numpy as np import numpy as np
from optparse import OptionParser, OptionGroup from optparse import OptionParser
from shutil import copy2 from shutil import copy2
from re import split from re import split
import damask import damask
@ -14,26 +14,10 @@ scriptID = ' '.join([scriptName,damask.version])
def list_split(option, opt, value, parser): def list_split(option, opt, value, parser):
setattr(parser.values, option.dest, value.split(',')) setattr(parser.values, option.dest, value.split(','))
def execute(cmd,streamIn=None,wd='./'):
'''
executes a command in given directory and returns stdout and stderr for optional stdin
'''
initialPath=os.getcwd()
os.chdir(wd)
process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE)
if streamIn != None:
out,error = process.communicate(streamIn.read())
else:
out,error = process.communicate()
os.chdir(initialPath)
return out,error
#--------------------------------------------------------------------------------------------------- #---------------------------------------------------------------------------------------------------
class myThread (threading.Thread): class myThread (threading.Thread):
#--------------------------------------------------------------------------------------------------- """Runner"""
'''
Runner class
'''
def __init__(self, threadID): def __init__(self, threadID):
threading.Thread.__init__(self) threading.Thread.__init__(self)
self.threadID = threadID self.threadID = threadID
@ -48,8 +32,6 @@ class myThread (threading.Thread):
s.release() s.release()
def doSim(delay,thread): def doSim(delay,thread):
# s.acquire() and s.release() are couple
#
global dirCurrent global dirCurrent
s.acquire() s.acquire()
delta_angle = offsetPhi() delta_angle = offsetPhi()
@ -63,22 +45,22 @@ def doSim(delay,thread):
os.mkdir(dire,0755) os.mkdir(dire,0755)
for file in [options.geometry+'.geom',options.load+'.load','numerics.config']: for file in [options.geometry+'.geom',options.load+'.load','numerics.config']:
copy2(dirCurrent+'/'+file, dire) copy2(dirCurrent+'/'+file, dire)
newMatConfig = newMaterialConfig(dirCurrent,delta_angle) newMaterialConfig(dirCurrent,delta_angle)
os.chdir(dire) os.chdir(dire)
if not os.path.isfile('%s_%s.spectralOut'%(options.geometry,options.load)): if not os.path.isfile('%s_%s.spectralOut'%(options.geometry,options.load)):
print('starting uniaxial tension in direction of angle %s from %s'%(file_angle,thread)) print('starting uniaxial tension in direction of angle %s from %s'%(file_angle,thread))
s.release() s.release()
execute('DAMASK_spectral -g %s -l %s'%(options.geometry,options.load)) damask.util.execute('DAMASK_spectral -g %s -l %s'%(options.geometry,options.load))
else: s.release() else: s.release()
s.acquire() s.acquire()
if not os.path.isfile('./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load)): if not os.path.isfile('./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load)):
print('starting post processing for angle %s from %s'%(file_angle,thread)) print('starting post processing for angle %s from %s'%(file_angle,thread))
s.release() s.release()
execute('postResults --cr f,p -d %s %s_%s.spectralOut'%('Rvalues',options.geometry,options.load)) damask.util.execute('postResults --cr f,p -d %s %s_%s.spectralOut'%('Rvalues',options.geometry,options.load))
execute('addCauchy ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load)) damask.util.execute('addCauchy ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
execute('addStrainTensors -l -v ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load)) damask.util.execute('addStrainTensors -l -v ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
print('post processing for angle %s from %s is finished'%(file_angle,thread)) print('post processing for angle %s from %s is finished'%(file_angle,thread))
else: else:
@ -122,7 +104,6 @@ def newMaterialConfig(dire,angle):
line2 = line line2 = line
f.write(line2) f.write(line2)
f.close() f.close()
return True
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN # MAIN
@ -135,16 +116,21 @@ strength anisotropic coefficients (normalized yield stress)
""", version=string.replace(scriptID,'\n','\\n') """, version=string.replace(scriptID,'\n','\\n')
) )
parser.add_option('-l','--load' , dest='load', type='string', parser.add_option('-l','--load' ,
help='name of the load file [%default]', metavar='string') dest='load', type='string',
parser.add_option('-g','--geometry', dest='geometry', type='string', help='name of the load file [%default]', metavar='string')
help='name of the geometry file [%default]', metavar='string') parser.add_option('-g','--geometry',
parser.add_option('-s', '--strain', dest='strain', type='string', action='callback', callback=list_split, dest='geometry', type='string',
help='the threshold strains, using comma to seperate multiple strains [%default]', metavar='string') help='name of the geometry file [%default]', metavar='string')
parser.add_option('-t','--threads', dest='threads', type='int', parser.add_option('-s', '--strain',
help='number of parallel executions [%default]', metavar='int') dest='strain', type='string', action='callback', callback=list_split,
parser.add_option('-n','--number', dest='number', type='int', help='threshold strains, using comma to seperate multiple strains [%default]', metavar='string')
help='Number of uni-axial tensile tests [%default]', metavar='int') parser.add_option('-t','--threads',
dest='threads', type='int',
help='number of parallel executions [%default]', metavar='int')
parser.add_option('-n','--number',
dest='number', type='int',
help='Number of uni-axial tensile tests [%default]', metavar='int')
parser.set_defaults(geometry = '20grains16x16x16') parser.set_defaults(geometry = '20grains16x16x16')
parser.set_defaults(load = 'tensionX') parser.set_defaults(load = 'tensionX')
@ -248,4 +234,4 @@ for i in xrange(2):
aniso_list_ang_strain.append('none') aniso_list_ang_strain.append('none')
writeformat = writeformat+'%-12s' writeformat = writeformat+'%-12s'
f.write('%-10s'%file_angle + writeformat%(tuple(aniso_list_ang_strain))+'\n') f.write('%-10s'%file_angle + writeformat%(tuple(aniso_list_ang_strain))+'\n')
f.close() f.close()

30
processing/misc/gwyddion_filter.py
View File

@ -1,33 +1,15 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,scipy.ndimage,scipy.signal,vtk import os,string,scipy
import numpy as np
import damask import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
#-------------------------------------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Apply filter(s) to Gwyddion data. Apply filter(s) to Gwyddion data.
""" + string.replace(scriptID,'\n','\\n') """ + string.replace(scriptID,'\n','\\n')
) )
@ -59,7 +41,7 @@ for file in filenames:
if pieces[1] == 'Height:': height = float(pieces[2]) if pieces[1] == 'Height:': height = float(pieces[2])
header.append(line.lstrip('#').strip()) header.append(line.lstrip('#').strip())
elevation = numpy.loadtxt(file)#*1e6 elevation = np.loadtxt(file)#*1e6
if options.opening > 0: if options.opening > 0:
elevation = scipy.ndimage.morphology.grey_opening(elevation,options.opening) elevation = scipy.ndimage.morphology.grey_opening(elevation,options.opening)
@ -80,5 +62,5 @@ for file in filenames:
elevation = scipy.ndimage.filters.median_filter(elevation,options.median) elevation = scipy.ndimage.filters.median_filter(elevation,options.median)
filters += '_median%i'%options.median filters += '_median%i'%options.median
numpy.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header)) np.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header))

36
processing/misc/vtk_fromGwyddion.py
View File

@ -1,9 +1,10 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,scipy.ndimage,scipy.signal,vtk import os,string,vtk
import numpy as np
import damask import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
@ -26,26 +27,7 @@ scalingFactor = { \
}, },
} }
#-------------------------------------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Produce VTK rectilinear grid from Gwyddion dataset exported as text. Produce VTK rectilinear grid from Gwyddion dataset exported as text.
""" + string.replace(scriptID,'\n','\\n') """ + string.replace(scriptID,'\n','\\n')
) )
@ -78,16 +60,16 @@ for file in filenames:
if options.scaling == 0.0: if options.scaling == 0.0:
options.scaling = scalingFactor[lateralunit][elevationunit] options.scaling = scalingFactor[lateralunit][elevationunit]
elevation = numpy.loadtxt(file)*options.scaling elevation = np.loadtxt(file)*options.scaling
grid = vtk.vtkRectilinearGrid() grid = vtk.vtkRectilinearGrid()
grid.SetDimensions(elevation.shape[1],elevation.shape[0],1) grid.SetDimensions(elevation.shape[1],elevation.shape[0],1)
xCoords = vtk.vtkDoubleArray() xCoords = vtk.vtkDoubleArray()
for x in numpy.arange(0.0,width,width/elevation.shape[1],'d'): for x in np.arange(0.0,width,width/elevation.shape[1],'d'):
xCoords.InsertNextValue(x) xCoords.InsertNextValue(x)
yCoords = vtk.vtkDoubleArray() yCoords = vtk.vtkDoubleArray()
for y in numpy.arange(0.0,height,height/elevation.shape[0],'d'): for y in np.arange(0.0,height,height/elevation.shape[0],'d'):
yCoords.InsertNextValue(y) yCoords.InsertNextValue(y)
zCoords = vtk.vtkDoubleArray() zCoords = vtk.vtkDoubleArray()
zCoords.InsertNextValue(0.0) zCoords.InsertNextValue(0.0)
@ -99,8 +81,8 @@ for file in filenames:
vector = vtk.vtkFloatArray() vector = vtk.vtkFloatArray()
vector.SetName("elevation"); vector.SetName("elevation");
vector.SetNumberOfComponents(3); vector.SetNumberOfComponents(3);
vector.SetNumberOfTuples(numpy.prod(elevation.shape)); vector.SetNumberOfTuples(np.prod(elevation.shape));
for i,z in enumerate(numpy.ravel(elevation)): for i,z in enumerate(np.ravel(elevation)):
vector.SetTuple3(i,0,0,z) vector.SetTuple3(i,0,0,z)
grid.GetPointData().AddArray(vector) grid.GetPointData().AddArray(vector)